Surrey and South Africa have suffered a major blow as Graeme Smith has been told to have an ankle operation that will rule him out for "a few months".

Smith will fly home for surgery after only a handful of matches in his new role as the captain of Surrey, and the injury also seems certain to rule him out of South Africa's quest for the Champions Trophy next month – when he had been due to play under the captaincy of AB de Villiers.

South Africa have already suffered one significant withdrawal from their squad, of Jacques Kallis for personal problems – although Smith's absence will surely prompt them to make a fresh approach to the veteran all-rounder to play.

Surrey issued a statement confirming that Smith would be absent from their Division One fixture against Durham that starts at The Oval on Thursday, and revealing he had suffered the ankle injury when playing international cricket in the winter.

Smith was quoted as saying: "To have to head home now, so early in my time at Surrey is very frustrating but I leave the team in a good place and hope to be back with them as soon as possible."

Chris Adams, Surrey's team director, said: "Graeme has made an impressive start as a leader and the squad have really responded to his leadership. It's clearly disappointing for all, especially Graeme, but we wish him a speedy recovery."

Smith's signing was especially significant as Surrey attempted to transform the culture of the club after a traumatic 2012. Gareth Batty, who succeeded Rory Hamilton-Brown as captain after the death of Tom Maynard last summer, is expected to resume in Smith's absence.